Research workbench
The complex structure of JMJD2A and monomethylated H3K36 peptide
Analyse The complex structure of JMJD2A and monomethylated H3K36 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PXJ
- Type
- protein
- Length
- 695 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jmjc domain-containing histone demethylation protein 3A; Monomethylated histone H3K36…
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- OGA, ZN, FE2
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.-) | protein | 347 | 29% helix, 24% strand | O75164 |
| B | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.-) | protein | 337 | 30% helix, 26% strand | O75164 |
| I | Monomethylated histone H3K36 peptide | protein | 5 | 0% helix, 0% strand | — |
| J | Monomethylated histone H3K36 peptide | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, I, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.76 | 0.80 | 80 | FE2, OGA |
| 2 | 371 | 0.73 | 0.84 | 44 | FE2, OGA |
| 3 | 351 | 0.57 | 0.75 | 41 | empty |
| 4 | 72 | 0.46 | 0.82 | 21 | empty |
| 5 | 72 | 0.45 | 0.82 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–J · 597 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 522 Ų buried · 2 hydrogen bonds · protein-protein
- A–I · 504 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 2PXJ · The complex structure of JMJD2A and monomethylated H3K36 peptide · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O75164
- Elsewhere: RCSB PDB 2PXJ · PDBe 2PXJ · UniProt O75164
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